Tamburini_AVIDseq

d2_DC

Cell type markers

# Cell type colors
cell_types <- sobj@meta.data %>%
  pull(!!sym(cell_type_id)) %>%
  unique()

names(cell_types) <- cell_types

type_cols <- theme_cols
names(type_cols) <- cell_types
type_cols <- type_cols[!is.na(names(type_cols))]

# # Find all cell type markers
# Idents(sobj) <- sobj %>%
#   FetchData(cell_type_id)
# 
# all_type_marks <- sobj %>%
#   FindAllMarkers(only.pos = T) %>%
#   as_tibble() %>%
#   filter(p_val_adj < 0.05)
# 
# # Cell type UMAP
# type_umap <- sobj %>%
#   plot_features(
#     feature     = cell_type_id,
#     plot_cols   = type_cols,
#     feat_levels = names(type_cols)
#   ) +
#   guides(color = col_guide) +
#   blank_theme +
#   theme(
#     legend.position = "top",
#     legend.title    = element_blank(),
#     legend.text     = element_text(size = 10)
#   )
# 
# # Marker plots
# for (i in seq_along(type_cols)) {
#   cat("\n#### ", names(type_cols[i]), "\n", sep = "")
#   
#   type_marks <- all_type_marks %>%
#     filter(cluster == names(type_cols[i]))
#   
#   type_marks_fig <- sobj %>%
#     create_marker_fig(
#       input_markers = type_marks,
#       type_id       = cell_type_id,
#       input_umap    = type_umap,
#       umap_color    = type_cols[[i]],
#       box_colors    = type_cols
#     )
#   
#   # type_marks %>%
#   #   kable() %>%
#   #   kable_styling(fixed_thead = T) %>%
#   #   print()
# 
#   print(type_marks_fig)
#   cat("\n\n---\n\n<br>\n\n<br>\n\n")
# }

Cell cluster markers

# Cell type colors
cell_clusts <- sobj@meta.data %>%
  mutate(
    type_clust = str_extract(!!sym(cluster_id), "^[0-9]+"),
    type_clust = as.numeric(type_clust)
  ) %>%
  arrange(!!sym(cell_type_id), type_clust) %>%
  pull(!!sym(cluster_id)) %>%
  unique()

names(cell_clusts) <- cell_clusts

clust_cols <- theme_cols
names(clust_cols) <- cell_clusts
clust_cols <- clust_cols[!is.na(names(clust_cols))]

# # Find all cell cluster markers
# Idents(sobj) <- sobj %>%
#   FetchData(cluster_id)
# 
# all_clust_marks <- sobj %>%
#   FindAllMarkers(only.pos = T) %>%
#   as_tibble() %>%
#   filter(p_val_adj < 0.05)
# 
# # Cluster UMAP
# clust_umap <- sobj %>%
#   plot_features(
#     feature     = cluster_id,
#     plot_cols   = clust_cols,
#     feat_levels = names(clust_cols)
#   ) +
#   guides(color = col_guide) +
#   blank_theme +
#   theme(
#     legend.position = "top",
#     legend.title    = element_blank(),
#     legend.text     = element_text(size = 10)
#   )
# 
# # Cluster plots
# for (i in seq_along(clust_cols)) {
#   cat("\n#### ", names(clust_cols[i]), "\n", sep = "")
#   
#   clust_marks <- all_clust_marks %>%
#     filter(cluster == names(clust_cols[i]))
#   
#   clust_marks_fig <- sobj %>%
#     create_marker_fig(
#       input_markers = clust_marks,
#       type_id       = cluster_id,
#       input_umap    = clust_umap,
#       umap_color    = clust_cols[[i]],
#       box_colors    = clust_cols
#     )
#   
#   print(clust_marks_fig)
#   cat("\n\n---\n\n<br>\n\n<br>\n\n")
# }

Separate cell cluster markers

# Find cluster markers separately for each cell type
sep_clust_marks <- cell_types %>%
  map(find_sep_clust_markers, sobj) %>%
  compact() %>%
  bind_rows()

sep_clusts <- sep_clust_marks$cluster %>%
  unique()

sep_clusts <- clust_cols[names(clust_cols) %in% sep_clusts] %>%
  names()

# Cluster plots
for (i in seq_along(sep_clusts)) {
  cat("\n#### ", sep_clusts[i], "\n", sep = "")
  
  sep_marks <- sep_clust_marks %>%
    filter(cluster == sep_clusts[i])
  
  type <- sep_clusts[i] %>%
    str_remove("^[0-9]+-")
  
  sep_cols <- clust_cols[grepl(str_c("-", type), names(clust_cols))]
  sep_cols <- c( "Other" = "#f0f0f0", sep_cols)
  
  sep_clust_umap <- sobj %>%
    FetchData(c("UMAP_1", "UMAP_2", cell_type_id, cluster_id)) %>%
    as_tibble(rownames = "cell_id") %>%
    mutate(!!sym(cluster_id) := if_else(!!sym(cluster_id) != type, "Other", !!sym(cluster_id))) %>%
    plot_features(
      feature     = cluster_id,
      plot_cols   = sep_cols,
      feat_levels = names(sep_cols)
    ) +
    guides(color = col_guide) +
    blank_theme +
    theme(
      legend.position = "top",
      legend.title    = element_blank(),
      legend.text     = element_text(size = 10)
    )
  
  sep_clust_marks_fig <- sobj %>%
    create_marker_fig(
      input_markers  = sep_marks,
      type_id        = cluster_id,
      input_umap     = sep_clust_umap,
      umap_color     = sep_cols[sep_clusts[i]],
      box_colors     = sep_cols,
      cell_type      = type
    )
  
  print(sep_clust_marks_fig)
  cat("\n\n---\n\n<br>\n\n<br>\n\n")
}

0-CCR7hi mig cDC2

---

6-CCR7hi mig cDC2

---

7-CCR7hi mig cDC2

---

12-CCR7hi mig cDC2

---

9-cDC1

---

14-cDC1

---

16-cDC1

---

1-cDC2 Tbet-

---

2-cDC2 Tbet-

---

4-cDC2 Tbet-

---

8-cDC2 Tbet-

---

10-cDC2 Tbet-

---

13-cDC2 Tbet-

---

15-cDC2 Tbet-

---